Locus 8076

Sequence ID 3R_DroMel_CAF1
Location 21,686,981 – 21,687,117
Length 136
Max. P 0.990963
window13002 window13003 window13004

overview

Window 2

Location 21,686,981 – 21,687,090
Length 109
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 88.15
Mean single sequence MFE -35.03
Consensus MFE -27.80
Energy contribution -28.57
Covariance contribution 0.78
Combinations/Pair 1.06
Mean z-score -3.17
Structure conservation index 0.79
SVM decision value 1.03
SVM RNA-class probability 0.903132
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21686981 109 + 27905053
CUAUUUUGGCAGUUUCCUUACAAGGCUUUUUGUUGGCCUGGCCAACAAUGAAGUCAGUUUCUUGUUGGCCAUUGCCAAAAAUAACUGCAUUUUCUGGACGAGGGAGUUA
...((((((((((.........(((((.......)))))(((((((((.((((....)))))))))))))))))))))))........(((..((.....))..))).. ( -37.30)
>DroPse_CAF1 76950 94 + 1
CUAUUUUGGCAGUUUUCU------------UGUUGG-CUGGCCAACAAUGAAGCCAGUUUCUUGUUGGCCAUUGCCAGAAAUAACUGCAUUUUGUG--CGCGGGAGUUA
..(((((.((((((....------------..((((-(((((((((((.((((....))))))))))))))..)))))....))))((((...)))--))).))))).. ( -34.90)
>DroEre_CAF1 10865 109 + 1
CUAUUUUGGCAGUUUCCUUGCAGGGCUUUUUGUUGGCCUGGCCAACAAUGAAGUCAGUUUCUUGUUGGCCAAUGCCAAAAAUAACUGCAUUUUCUGGACGAGGGAGUUA
((.(((((.(((......(((((.........(((((.((((((((((.((((....))))))))))))))..)))))......)))))....)))..))))).))... ( -36.16)
>DroYak_CAF1 10996 109 + 1
CUAUUUUGGCAGUUUCCUUGCAAGGCUUUUUGUUAGCCUGGCCAACAAUGAAGUCAGUUUCUUGUUGGCCAUUGCCAAAAAUAACUGCAUUUUCUGGACGAGGGAGUUA
...((((((((((.........(((((.......)))))(((((((((.((((....)))))))))))))))))))))))........(((..((.....))..))).. ( -37.30)
>DroAna_CAF1 12063 109 + 1
CUAUUUUGGCAGUUUCCUUGUAACGCUUUUUGUUGGCCCGGCCAACAAUGAAGUCAGUUUCUUGUCGGCCAUUGCCAAAAAUAACUGCAUUUUCUGGACGAGGGAGUUA
............(((((((((...(((((((((((((...)))))))).)))))(((((..((...(((....)))..))..)))))..........)))))))))... ( -29.60)
>DroPer_CAF1 76706 94 + 1
CUAUUUUGGCAGUUUUCU------------UGUUGG-CUGGCCAACAAUGAAGCCAGUUUCUUGUUGGCCAUUGCCAGAAAUAACUGCAUUUUGUG--CGCGGGAGUUA
..(((((.((((((....------------..((((-(((((((((((.((((....))))))))))))))..)))))....))))((((...)))--))).))))).. ( -34.90)
>consensus
CUAUUUUGGCAGUUUCCUUGCAAGGCUUUUUGUUGGCCUGGCCAACAAUGAAGUCAGUUUCUUGUUGGCCAUUGCCAAAAAUAACUGCAUUUUCUGGACGAGGGAGUUA
...((((((((((...........(((.......)))..(((((((((.((((....))))))))))))))))))))))).(((((.(..............).))))) (-27.80 = -28.57 +   0.78)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,686,981 – 21,687,090
Length 109
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 88.15
Mean single sequence MFE -31.92
Consensus MFE -26.53
Energy contribution -26.58
Covariance contribution 0.06
Combinations/Pair 1.09
Mean z-score -3.94
Structure conservation index 0.83
SVM decision value 2.24
SVM RNA-class probability 0.990963
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21686981 109 - 27905053
UAACUCCCUCGUCCAGAAAAUGCAGUUAUUUUUGGCAAUGGCCAACAAGAAACUGACUUCAUUGUUGGCCAGGCCAACAAAAAGCCUUGUAAGGAAACUGCCAAAAUAG
.....................((((((....(((((..(((((((((((((......))).)))))))))).))))).......(((....))).))))))........ ( -33.20)
>DroPse_CAF1 76950 94 - 1
UAACUCCCGCG--CACAAAAUGCAGUUAUUUCUGGCAAUGGCCAACAAGAAACUGGCUUCAUUGUUGGCCAG-CCAACA------------AGAAAACUGCCAAAAUAG
...........--........((((((.(((.((((..(((((((((((((......))).)))))))))))-)))...------------))).))))))........ ( -30.10)
>DroEre_CAF1 10865 109 - 1
UAACUCCCUCGUCCAGAAAAUGCAGUUAUUUUUGGCAUUGGCCAACAAGAAACUGACUUCAUUGUUGGCCAGGCCAACAAAAAGCCCUGCAAGGAAACUGCCAAAAUAG
....................(((((...((((((((.((((((((((((((......))).)))))))))))))))...))))...)))))((....)).......... ( -34.30)
>DroYak_CAF1 10996 109 - 1
UAACUCCCUCGUCCAGAAAAUGCAGUUAUUUUUGGCAAUGGCCAACAAGAAACUGACUUCAUUGUUGGCCAGGCUAACAAAAAGCCUUGCAAGGAAACUGCCAAAAUAG
.....................((((((.((((((.((((((((((((((((......))).))))))))))((((.......)))))))))))))))))))........ ( -34.60)
>DroAna_CAF1 12063 109 - 1
UAACUCCCUCGUCCAGAAAAUGCAGUUAUUUUUGGCAAUGGCCGACAAGAAACUGACUUCAUUGUUGGCCGGGCCAACAAAAAGCGUUACAAGGAAACUGCCAAAAUAG
...........(((....(((((..((....(((((..(((((((((((((......))).)))))))))).)))))..))..)))))....))).............. ( -29.20)
>DroPer_CAF1 76706 94 - 1
UAACUCCCGCG--CACAAAAUGCAGUUAUUUCUGGCAAUGGCCAACAAGAAACUGGCUUCAUUGUUGGCCAG-CCAACA------------AGAAAACUGCCAAAAUAG
...........--........((((((.(((.((((..(((((((((((((......))).)))))))))))-)))...------------))).))))))........ ( -30.10)
>consensus
UAACUCCCUCGUCCAGAAAAUGCAGUUAUUUUUGGCAAUGGCCAACAAGAAACUGACUUCAUUGUUGGCCAGGCCAACAAAAAGCCUUGCAAGGAAACUGCCAAAAUAG
.............................(((((((..(((((((((((((......))).))))))))))....................((....)))))))))... (-26.53 = -26.58 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,687,020 – 21,687,117
Length 97
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 89.78
Mean single sequence MFE -32.06
Consensus MFE -24.13
Energy contribution -24.93
Covariance contribution 0.81
Combinations/Pair 1.07
Mean z-score -2.92
Structure conservation index 0.75
SVM decision value 0.03
SVM RNA-class probability 0.548696
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21687020 97 + 27905053
GGCCAACAAUGAAGUCAGUUUCUUGUUGGCCAUUGCCAAAAAUAACUGCAUUUUCUGGACGAGGGAGUUAGUAAAACUUUCCC-CAUACCCGGAAGUG
(((((((((.((((....)))))))))))))....................(((((((....(((.(..((.....))..)))-)....))))))).. ( -29.80)
>DroPse_CAF1 76976 95 + 1
GGCCAACAAUGAAGCCAGUUUCUUGUUGGCCAUUGCCAGAAAUAACUGCAUUUUGUG--CGCGGGAGUUACGAAAACUUUCUC-UCUGCACGGAAAUG
(((((((((.((((....)))))))))))))..(((.((......)))))(((((((--((.(((((.............)))-)))))))))))... ( -34.82)
>DroSec_CAF1 10009 96 + 1
GGCCAACAAUGAAGUCAGUUUCUUGUUGGCCAUUGCCAA-AAUAACUGCAUUUUCUGGACGAGGGAGUUAGUAAAACUUUCCC-CAUGCCCGGAAGUG
(((((((((.((((....)))))))))))))..(((...-.......))).(((((((.((.(((.(..((.....))..)))-).)).))))))).. ( -32.10)
>DroEre_CAF1 10904 97 + 1
GGCCAACAAUGAAGUCAGUUUCUUGUUGGCCAAUGCCAAAAAUAACUGCAUUUUCUGGACGAGGGAGUUAGUAAAACUUUCUA-CAUGCCCGGAAGUG
(((((((((.((((....))))))))))))).................(((((((.((...((..((((.....))))..)).-....)).))))))) ( -31.70)
>DroAna_CAF1 12102 98 + 1
GGCCAACAAUGAAGUCAGUUUCUUGUCGGCCAUUGCCAAAAAUAACUGCAUUUUCUGGACGAGGGAGUUACUAAAACUUUUCCCCUGGCCCGGAAGUG
((((.((((.((((....)))))))).))))....................(((((((.(.((((((((.....))))....)))).).))))))).. ( -29.10)
>DroPer_CAF1 76732 95 + 1
GGCCAACAAUGAAGCCAGUUUCUUGUUGGCCAUUGCCAGAAAUAACUGCAUUUUGUG--CGCGGGAGUUACGAAAACUUUCUC-UCUGCACGGAAAUG
(((((((((.((((....)))))))))))))..(((.((......)))))(((((((--((.(((((.............)))-)))))))))))... ( -34.82)
>consensus
GGCCAACAAUGAAGUCAGUUUCUUGUUGGCCAUUGCCAAAAAUAACUGCAUUUUCUGGACGAGGGAGUUACUAAAACUUUCCC_CAUGCCCGGAAGUG
(((((((((.((((....))))))))))))).................(((((((.((....(..((((.....))))..).......)).))))))) (-24.13 = -24.93 +   0.81)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:02:03 2006